If you want further confirmation, the strip starts with a clear view that they are off the ship. The illusions started upon their entry into the vessel, Wally lost his Dittos, but only when they where practically touching that hunk of metal.
Basically, the thing is starving. That’s why it replicated Lin and sought new personalities to replicate. What we see outside the ship is real, and the real Holly knows she’s committed irreparable damage. I’ll also link the panel that further reinforces this theory. (When they first see her before she mutated.) i.e. “God.. Have I ever REALLY known her?”